Starting phenix.real_space_refine on Sat Aug 3 17:05:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zje_60142/08_2024/8zje_60142_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zje_60142/08_2024/8zje_60142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zje_60142/08_2024/8zje_60142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zje_60142/08_2024/8zje_60142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zje_60142/08_2024/8zje_60142_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zje_60142/08_2024/8zje_60142_neut.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5571 2.51 5 N 1504 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "S GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8743 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1810 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2570 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2142 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1726 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Unusual residues: {'ACY': 1, 'XZA': 1} Classifications: {'peptide': 8, 'undetermined': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 6, None: 3} Not linked: pdbres="ACY C 1 " pdbres="DTY C 2 " Not linked: pdbres="PHE C 6 " pdbres="XZA C 7 " Not linked: pdbres="XZA C 7 " pdbres="LEU C 8 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'ACY:plan-1': 1, 'NMM:plan-2': 1, 'HYP:plan-1': 1, 'XZA:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.62 Number of scatterers: 8743 At special positions: 0 Unit cell: (94.9, 115.34, 129.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1612 8.00 N 1504 7.00 C 5571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY C 2 " Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 39.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.695A pdb=" N GLN A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.549A pdb=" N LEU A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 10 through 31 removed outlier: 4.355A pdb=" N GLN B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.838A pdb=" N ILE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 54 through 58 removed outlier: 4.243A pdb=" N ASN G 58 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 68 removed outlier: 4.592A pdb=" N LEU R 47 " --> pdb=" O TRP R 43 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 95 Processing helix chain 'R' and resid 97 through 103 removed outlier: 4.143A pdb=" N LEU R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 removed outlier: 3.626A pdb=" N ASN R 119 " --> pdb=" O CYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 Processing helix chain 'R' and resid 175 through 180 removed outlier: 4.060A pdb=" N ALA R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 213 Processing helix chain 'R' and resid 213 through 234 Processing helix chain 'R' and resid 242 through 253 Processing helix chain 'R' and resid 253 through 289 removed outlier: 3.871A pdb=" N ARG R 258 " --> pdb=" O ALA R 254 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG R 263 " --> pdb=" O ALA R 259 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 298 through 324 removed outlier: 3.523A pdb=" N SER R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'S' and resid 52 through 55 removed outlier: 4.015A pdb=" N GLY S 55 " --> pdb=" O SER S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 55' Processing helix chain 'S' and resid 86 through 90 removed outlier: 3.603A pdb=" N THR S 90 " --> pdb=" O SER S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 6.405A pdb=" N LEU A 34 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 206 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 36 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N SER A 227 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS A 35 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N MET A 229 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 37 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 231 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 228 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 274 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 230 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A 276 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 232 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 3.626A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.537A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.806A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.327A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.678A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.656A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.309A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'S' and resid 2 through 5 Processing sheet with id=AB2, first strand: chain 'S' and resid 9 through 11 removed outlier: 6.018A pdb=" N ARG S 37 " --> pdb=" O TRP S 46 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP S 46 " --> pdb=" O ARG S 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.771A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1409 1.31 - 1.43: 2489 1.43 - 1.56: 4943 1.56 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8924 Sorted by residual: bond pdb=" CA ARG A 29 " pdb=" C ARG A 29 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.28e-02 6.10e+03 2.96e+01 bond pdb=" CA VAL A 201 " pdb=" CB VAL A 201 " ideal model delta sigma weight residual 1.548 1.479 0.068 1.46e-02 4.69e+03 2.19e+01 bond pdb=" N VAL A 201 " pdb=" CA VAL A 201 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.17e-02 7.31e+03 1.47e+01 bond pdb=" CA GLU A 33 " pdb=" C GLU A 33 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.17e-02 7.31e+03 1.44e+01 bond pdb=" CA GLU A 28 " pdb=" C GLU A 28 " ideal model delta sigma weight residual 1.522 1.474 0.047 1.25e-02 6.40e+03 1.43e+01 ... (remaining 8919 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 244 107.06 - 113.80: 4955 113.80 - 120.54: 3538 120.54 - 127.29: 3272 127.29 - 134.03: 101 Bond angle restraints: 12110 Sorted by residual: angle pdb=" N ARG A 29 " pdb=" CA ARG A 29 " pdb=" C ARG A 29 " ideal model delta sigma weight residual 112.94 102.00 10.94 1.41e+00 5.03e-01 6.02e+01 angle pdb=" N GLU A 28 " pdb=" CA GLU A 28 " pdb=" C GLU A 28 " ideal model delta sigma weight residual 114.09 102.20 11.89 1.55e+00 4.16e-01 5.89e+01 angle pdb=" N ARG A 31 " pdb=" CA ARG A 31 " pdb=" C ARG A 31 " ideal model delta sigma weight residual 113.41 104.83 8.58 1.22e+00 6.72e-01 4.94e+01 angle pdb=" N HYP C 3 " pdb=" CA HYP C 3 " pdb=" CB HYP C 3 " ideal model delta sigma weight residual 103.00 109.27 -6.27 1.10e+00 8.26e-01 3.25e+01 angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 111.55 105.34 6.21 1.37e+00 5.33e-01 2.06e+01 ... (remaining 12105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4738 17.96 - 35.92: 410 35.92 - 53.87: 96 53.87 - 71.83: 11 71.83 - 89.79: 11 Dihedral angle restraints: 5266 sinusoidal: 1973 harmonic: 3293 Sorted by residual: dihedral pdb=" CA THR B 254 " pdb=" C THR B 254 " pdb=" N CYS B 255 " pdb=" CA CYS B 255 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LYS B 83 " pdb=" C LYS B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA THR B 170 " pdb=" C THR B 170 " pdb=" N CYS B 171 " pdb=" CA CYS B 171 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1331 0.103 - 0.207: 50 0.207 - 0.310: 2 0.310 - 0.414: 2 0.414 - 0.517: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA HYP C 3 " pdb=" N HYP C 3 " pdb=" C HYP C 3 " pdb=" CB HYP C 3 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA THR A 226 " pdb=" N THR A 226 " pdb=" C THR A 226 " pdb=" CB THR A 226 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1383 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD NMM C 9 " -0.066 2.00e-02 2.50e+03 1.51e-01 3.41e+02 pdb=" NE NMM C 9 " 0.223 2.00e-02 2.50e+03 pdb=" CZ NMM C 9 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 NMM C 9 " -0.088 2.00e-02 2.50e+03 pdb=" NH2 NMM C 9 " -0.212 2.00e-02 2.50e+03 pdb=" CAA NMM C 9 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 197 " 0.027 2.00e-02 2.50e+03 5.60e-02 3.14e+01 pdb=" C ASP A 197 " -0.097 2.00e-02 2.50e+03 pdb=" O ASP A 197 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 198 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 319 " 0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO R 320 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO R 320 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 320 " 0.050 5.00e-02 4.00e+02 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 912 2.74 - 3.28: 8882 3.28 - 3.82: 14382 3.82 - 4.36: 17199 4.36 - 4.90: 30801 Nonbonded interactions: 72176 Sorted by model distance: nonbonded pdb=" O THR B 91 " pdb=" OG1 THR B 92 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B 279 " pdb=" O VAL B 320 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 286 " pdb=" OD2 ASP G 47 " model vdw 2.251 3.040 nonbonded pdb=" O ALA R 128 " pdb=" OG1 THR R 132 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.257 3.040 ... (remaining 72171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8924 Z= 0.328 Angle : 0.714 11.891 12110 Z= 0.417 Chirality : 0.047 0.517 1386 Planarity : 0.006 0.151 1530 Dihedral : 14.594 89.791 3138 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.33 % Allowed : 14.46 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1104 helix: 2.42 (0.26), residues: 393 sheet: -0.05 (0.32), residues: 288 loop : -0.06 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 10 HIS 0.004 0.001 HIS R 309 PHE 0.022 0.001 PHE A 222 TYR 0.022 0.001 TYR S 190 ARG 0.006 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.062 Fit side-chains REVERT: A 28 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7892 (pt0) REVERT: A 310 PHE cc_start: 0.8285 (t80) cc_final: 0.8058 (t80) REVERT: A 325 ILE cc_start: 0.8491 (tp) cc_final: 0.8271 (tt) REVERT: A 358 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: B 64 TYR cc_start: 0.9036 (m-80) cc_final: 0.8749 (m-80) REVERT: B 231 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7634 (mp0) REVERT: B 267 MET cc_start: 0.8377 (ttm) cc_final: 0.7934 (ttm) REVERT: B 306 LYS cc_start: 0.8289 (mmmm) cc_final: 0.8016 (mmtt) REVERT: S 5 GLU cc_start: 0.8598 (mp0) cc_final: 0.7707 (mp0) REVERT: S 67 PHE cc_start: 0.8173 (m-10) cc_final: 0.7833 (m-10) REVERT: S 81 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7138 (tp40) REVERT: S 223 ASP cc_start: 0.7616 (m-30) cc_final: 0.7307 (m-30) REVERT: C 10 TRP cc_start: 0.7882 (OUTLIER) cc_final: 0.7582 (p90) outliers start: 3 outliers final: 0 residues processed: 153 average time/residue: 0.2592 time to fit residues: 52.0184 Evaluate side-chains 140 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain C residue 10 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.0670 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 18 GLN B 22 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 GLN R 208 ASN R 295 HIS S 183 GLN S 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8924 Z= 0.302 Angle : 0.590 8.109 12110 Z= 0.316 Chirality : 0.044 0.180 1386 Planarity : 0.004 0.058 1530 Dihedral : 5.617 59.350 1239 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.97 % Allowed : 14.02 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1104 helix: 2.31 (0.26), residues: 397 sheet: -0.10 (0.32), residues: 276 loop : -0.07 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 174 HIS 0.005 0.001 HIS R 181 PHE 0.020 0.002 PHE A 49 TYR 0.028 0.002 TYR S 190 ARG 0.003 0.001 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.029 Fit side-chains REVERT: A 259 THR cc_start: 0.8529 (m) cc_final: 0.8239 (p) REVERT: A 289 HIS cc_start: 0.8030 (m-70) cc_final: 0.7819 (m-70) REVERT: A 305 GLN cc_start: 0.7496 (tp-100) cc_final: 0.7040 (tp-100) REVERT: A 358 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: B 231 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7563 (mp0) REVERT: R 58 VAL cc_start: 0.8324 (p) cc_final: 0.8109 (m) REVERT: R 190 TYR cc_start: 0.7029 (m-80) cc_final: 0.6411 (m-80) REVERT: R 325 PHE cc_start: 0.7438 (m-10) cc_final: 0.7067 (m-10) REVERT: R 336 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.5398 (ttt180) REVERT: S 42 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7722 (mptt) REVERT: S 81 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7265 (tp40) REVERT: S 92 MET cc_start: 0.8467 (ttm) cc_final: 0.7999 (tpp) REVERT: C 10 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7872 (p90) outliers start: 18 outliers final: 5 residues processed: 161 average time/residue: 0.2248 time to fit residues: 48.6115 Evaluate side-chains 150 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain C residue 10 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 GLN S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8924 Z= 0.400 Angle : 0.615 8.224 12110 Z= 0.328 Chirality : 0.045 0.195 1386 Planarity : 0.004 0.051 1530 Dihedral : 5.617 57.989 1239 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.29 % Allowed : 15.33 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1104 helix: 2.13 (0.26), residues: 396 sheet: -0.27 (0.31), residues: 280 loop : -0.16 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 87 HIS 0.006 0.001 HIS R 309 PHE 0.019 0.002 PHE B 240 TYR 0.027 0.002 TYR S 190 ARG 0.004 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 0.910 Fit side-chains REVERT: A 28 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7519 (pt0) REVERT: A 286 MET cc_start: 0.7884 (mmm) cc_final: 0.7667 (mmp) REVERT: A 358 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: B 202 ARG cc_start: 0.7892 (tpp80) cc_final: 0.7671 (ttm-80) REVERT: B 231 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7615 (mp0) REVERT: B 234 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8609 (mp) REVERT: B 267 MET cc_start: 0.8154 (mmm) cc_final: 0.7927 (ttm) REVERT: R 325 PHE cc_start: 0.7433 (m-10) cc_final: 0.7020 (m-10) REVERT: R 336 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.5163 (ttt180) REVERT: S 42 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7686 (mptt) REVERT: S 81 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7221 (tp40) REVERT: S 92 MET cc_start: 0.8498 (ttm) cc_final: 0.8024 (tpp) outliers start: 30 outliers final: 13 residues processed: 169 average time/residue: 0.2210 time to fit residues: 50.4015 Evaluate side-chains 156 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8924 Z= 0.155 Angle : 0.505 6.434 12110 Z= 0.268 Chirality : 0.040 0.152 1386 Planarity : 0.004 0.055 1530 Dihedral : 5.082 54.402 1237 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.41 % Allowed : 16.98 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1104 helix: 2.26 (0.25), residues: 397 sheet: -0.13 (0.31), residues: 280 loop : -0.12 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 174 HIS 0.002 0.001 HIS R 181 PHE 0.014 0.001 PHE A 49 TYR 0.015 0.001 TYR S 190 ARG 0.002 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 0.994 Fit side-chains REVERT: A 25 GLU cc_start: 0.7652 (tt0) cc_final: 0.7090 (tm-30) REVERT: A 259 THR cc_start: 0.8516 (m) cc_final: 0.8163 (p) REVERT: A 305 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7455 (tp-100) REVERT: A 358 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: B 194 SER cc_start: 0.8447 (m) cc_final: 0.8193 (p) REVERT: B 225 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7041 (mm-40) REVERT: B 231 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7615 (mp0) REVERT: B 234 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8519 (mp) REVERT: R 325 PHE cc_start: 0.7487 (m-10) cc_final: 0.6973 (m-10) REVERT: R 336 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5350 (ttt180) REVERT: S 19 LEU cc_start: 0.7742 (mt) cc_final: 0.7495 (mt) REVERT: S 42 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7639 (mptt) REVERT: S 81 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7207 (tp-100) REVERT: S 92 MET cc_start: 0.8419 (ttm) cc_final: 0.7966 (tpp) outliers start: 22 outliers final: 10 residues processed: 173 average time/residue: 0.2311 time to fit residues: 53.6604 Evaluate side-chains 157 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 20.0000 chunk 60 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 90 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8924 Z= 0.214 Angle : 0.523 6.502 12110 Z= 0.276 Chirality : 0.041 0.182 1386 Planarity : 0.004 0.055 1530 Dihedral : 5.039 55.480 1237 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.41 % Allowed : 16.98 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1104 helix: 2.30 (0.25), residues: 397 sheet: -0.22 (0.31), residues: 277 loop : -0.11 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.003 0.001 HIS R 309 PHE 0.014 0.001 PHE A 49 TYR 0.019 0.001 TYR S 190 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.983 Fit side-chains REVERT: A 25 GLU cc_start: 0.7676 (tt0) cc_final: 0.7128 (tm-30) REVERT: A 259 THR cc_start: 0.8533 (m) cc_final: 0.8242 (p) REVERT: A 358 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: B 24 ARG cc_start: 0.8541 (tmm-80) cc_final: 0.8203 (tmm-80) REVERT: B 225 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7044 (mm-40) REVERT: B 231 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7624 (mp0) REVERT: B 234 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 308 ASP cc_start: 0.7559 (m-30) cc_final: 0.6997 (p0) REVERT: R 325 PHE cc_start: 0.7469 (m-10) cc_final: 0.6929 (m-10) REVERT: R 336 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5238 (ttt180) REVERT: S 42 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7643 (mptt) REVERT: S 81 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7118 (tp-100) REVERT: S 92 MET cc_start: 0.8474 (ttm) cc_final: 0.7959 (tpp) REVERT: S 114 THR cc_start: 0.7781 (p) cc_final: 0.7417 (p) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.2229 time to fit residues: 48.1747 Evaluate side-chains 162 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8924 Z= 0.196 Angle : 0.518 7.093 12110 Z= 0.271 Chirality : 0.041 0.165 1386 Planarity : 0.004 0.054 1530 Dihedral : 4.932 55.109 1237 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.85 % Allowed : 17.09 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1104 helix: 2.37 (0.25), residues: 397 sheet: -0.28 (0.30), residues: 280 loop : -0.10 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.002 0.001 HIS S 34 PHE 0.014 0.001 PHE A 49 TYR 0.017 0.001 TYR S 190 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.055 Fit side-chains REVERT: A 25 GLU cc_start: 0.7655 (tt0) cc_final: 0.7102 (tm-30) REVERT: A 29 ARG cc_start: 0.8299 (mtm110) cc_final: 0.8084 (mtm110) REVERT: A 239 GLN cc_start: 0.8234 (mm110) cc_final: 0.7941 (mm110) REVERT: A 259 THR cc_start: 0.8519 (m) cc_final: 0.8228 (p) REVERT: A 358 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: B 24 ARG cc_start: 0.8545 (tmm-80) cc_final: 0.8189 (tmm-80) REVERT: B 81 ASP cc_start: 0.8656 (p0) cc_final: 0.8432 (p0) REVERT: B 225 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: B 231 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7585 (mp0) REVERT: B 234 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 308 ASP cc_start: 0.7595 (m-30) cc_final: 0.7019 (p0) REVERT: R 336 ARG cc_start: 0.5857 (OUTLIER) cc_final: 0.5322 (ttt180) REVERT: S 42 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7669 (mptt) REVERT: S 81 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7150 (tp-100) outliers start: 26 outliers final: 18 residues processed: 166 average time/residue: 0.2354 time to fit residues: 52.4484 Evaluate side-chains 162 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8924 Z= 0.154 Angle : 0.506 9.079 12110 Z= 0.262 Chirality : 0.040 0.201 1386 Planarity : 0.004 0.054 1530 Dihedral : 4.723 54.342 1237 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.18 % Allowed : 16.98 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1104 helix: 2.36 (0.25), residues: 401 sheet: -0.25 (0.30), residues: 281 loop : -0.13 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.002 0.000 HIS B 230 PHE 0.014 0.001 PHE S 67 TYR 0.022 0.001 TYR A 237 ARG 0.002 0.000 ARG R 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7663 (tt0) cc_final: 0.7137 (tm-30) REVERT: A 29 ARG cc_start: 0.8256 (mtm110) cc_final: 0.8051 (mtm110) REVERT: A 250 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7338 (ttm) REVERT: A 259 THR cc_start: 0.8516 (m) cc_final: 0.8241 (p) REVERT: A 286 MET cc_start: 0.7848 (mmm) cc_final: 0.7330 (mtt) REVERT: A 289 HIS cc_start: 0.7803 (m-70) cc_final: 0.7497 (m90) REVERT: B 225 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7194 (mm-40) REVERT: B 231 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7575 (mp0) REVERT: B 234 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 267 MET cc_start: 0.8245 (mmm) cc_final: 0.7974 (tpp) REVERT: B 275 ILE cc_start: 0.8347 (pp) cc_final: 0.7955 (mm) REVERT: R 214 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7674 (mp) REVERT: R 336 ARG cc_start: 0.5773 (OUTLIER) cc_final: 0.5317 (ttt180) REVERT: S 2 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8156 (mm-40) REVERT: S 42 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7665 (mptt) REVERT: S 81 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7180 (tp-100) REVERT: S 153 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7389 (mm-30) outliers start: 29 outliers final: 19 residues processed: 169 average time/residue: 0.2310 time to fit residues: 52.2738 Evaluate side-chains 165 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8924 Z= 0.149 Angle : 0.513 7.730 12110 Z= 0.263 Chirality : 0.040 0.196 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.625 53.590 1237 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.85 % Allowed : 17.74 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1104 helix: 2.42 (0.26), residues: 402 sheet: -0.19 (0.31), residues: 281 loop : -0.15 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.002 0.000 HIS S 34 PHE 0.031 0.001 PHE S 67 TYR 0.019 0.001 TYR A 237 ARG 0.002 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.014 Fit side-chains REVERT: A 25 GLU cc_start: 0.7662 (tt0) cc_final: 0.7141 (tm-30) REVERT: A 239 GLN cc_start: 0.8462 (mm110) cc_final: 0.8159 (mm110) REVERT: A 250 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7259 (ttm) REVERT: A 259 THR cc_start: 0.8504 (m) cc_final: 0.8245 (p) REVERT: A 289 HIS cc_start: 0.7803 (m-70) cc_final: 0.7507 (m90) REVERT: B 24 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.8224 (ttp-170) REVERT: B 225 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7234 (mm-40) REVERT: B 231 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7569 (mp0) REVERT: B 234 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8324 (mp) REVERT: B 267 MET cc_start: 0.8236 (mmm) cc_final: 0.7969 (tpp) REVERT: B 275 ILE cc_start: 0.8343 (pp) cc_final: 0.7936 (mm) REVERT: B 308 ASP cc_start: 0.7625 (m-30) cc_final: 0.7006 (p0) REVERT: R 214 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7687 (mp) REVERT: R 336 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5365 (ttt180) REVERT: S 2 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8164 (mm-40) REVERT: S 37 ARG cc_start: 0.7937 (ptt180) cc_final: 0.7528 (ptt90) REVERT: S 81 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7197 (tp-100) REVERT: S 153 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7408 (mm-30) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.2205 time to fit residues: 51.1253 Evaluate side-chains 169 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8924 Z= 0.170 Angle : 0.533 12.074 12110 Z= 0.270 Chirality : 0.040 0.185 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.603 53.717 1237 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.18 % Allowed : 17.42 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1104 helix: 2.42 (0.26), residues: 401 sheet: -0.18 (0.31), residues: 281 loop : -0.12 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.002 0.000 HIS S 34 PHE 0.027 0.001 PHE S 67 TYR 0.019 0.001 TYR A 237 ARG 0.015 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 0.960 Fit side-chains REVERT: A 25 GLU cc_start: 0.7662 (tt0) cc_final: 0.7161 (tm-30) REVERT: A 239 GLN cc_start: 0.8444 (mm110) cc_final: 0.8104 (mm110) REVERT: A 250 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7282 (ttm) REVERT: A 259 THR cc_start: 0.8459 (m) cc_final: 0.8201 (p) REVERT: A 286 MET cc_start: 0.7821 (mmm) cc_final: 0.7358 (mtt) REVERT: A 289 HIS cc_start: 0.7810 (m-70) cc_final: 0.7521 (m90) REVERT: B 24 ARG cc_start: 0.8480 (tmm-80) cc_final: 0.8203 (ttp-170) REVERT: B 225 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7232 (mm-40) REVERT: B 231 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7562 (mp0) REVERT: B 234 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 267 MET cc_start: 0.8222 (mmm) cc_final: 0.7972 (tpp) REVERT: B 274 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6115 (tp) REVERT: B 275 ILE cc_start: 0.8322 (pp) cc_final: 0.7922 (mm) REVERT: B 308 ASP cc_start: 0.7625 (m-30) cc_final: 0.7029 (p0) REVERT: R 214 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7697 (mp) REVERT: R 336 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.5237 (ttt180) REVERT: S 2 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8166 (mm-40) REVERT: S 37 ARG cc_start: 0.7906 (ptt180) cc_final: 0.7483 (ptt90) REVERT: S 81 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7175 (tp-100) REVERT: S 153 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7411 (mm-30) outliers start: 29 outliers final: 20 residues processed: 168 average time/residue: 0.2241 time to fit residues: 50.9986 Evaluate side-chains 171 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 171 ASN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8924 Z= 0.159 Angle : 0.525 11.629 12110 Z= 0.266 Chirality : 0.040 0.158 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.546 53.753 1237 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.96 % Allowed : 17.85 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1104 helix: 2.39 (0.26), residues: 402 sheet: -0.10 (0.31), residues: 275 loop : -0.12 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.002 0.000 HIS S 34 PHE 0.022 0.001 PHE S 67 TYR 0.019 0.001 TYR A 237 ARG 0.014 0.000 ARG A 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.089 Fit side-chains REVERT: A 25 GLU cc_start: 0.7672 (tt0) cc_final: 0.7169 (tm-30) REVERT: A 239 GLN cc_start: 0.8446 (mm110) cc_final: 0.8094 (mm110) REVERT: A 250 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7300 (ttm) REVERT: A 259 THR cc_start: 0.8477 (m) cc_final: 0.8201 (p) REVERT: A 286 MET cc_start: 0.7851 (mmm) cc_final: 0.7383 (mtt) REVERT: A 289 HIS cc_start: 0.7774 (m-70) cc_final: 0.7491 (m90) REVERT: B 24 ARG cc_start: 0.8464 (tmm-80) cc_final: 0.8223 (ttp-170) REVERT: B 225 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7260 (mm-40) REVERT: B 231 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7523 (mp0) REVERT: B 234 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8297 (mp) REVERT: B 267 MET cc_start: 0.8199 (mmm) cc_final: 0.7966 (tpp) REVERT: B 274 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6070 (tp) REVERT: B 275 ILE cc_start: 0.8321 (pp) cc_final: 0.7920 (mm) REVERT: B 308 ASP cc_start: 0.7637 (m-30) cc_final: 0.7014 (p0) REVERT: R 214 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7722 (mp) REVERT: R 336 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.5315 (ttt180) REVERT: S 2 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8180 (mm-40) REVERT: S 37 ARG cc_start: 0.7919 (ptt180) cc_final: 0.7465 (ptt90) REVERT: S 81 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7138 (tp-100) REVERT: S 153 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7429 (mm-30) outliers start: 27 outliers final: 19 residues processed: 169 average time/residue: 0.2257 time to fit residues: 51.4818 Evaluate side-chains 170 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0060 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.0870 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118499 restraints weight = 10496.763| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.10 r_work: 0.3309 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8924 Z= 0.136 Angle : 0.509 11.282 12110 Z= 0.257 Chirality : 0.040 0.167 1386 Planarity : 0.004 0.055 1530 Dihedral : 4.423 53.636 1237 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.85 % Allowed : 17.85 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1104 helix: 2.45 (0.26), residues: 400 sheet: -0.07 (0.31), residues: 280 loop : -0.05 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.002 0.000 HIS S 34 PHE 0.024 0.001 PHE R 334 TYR 0.018 0.001 TYR A 237 ARG 0.012 0.000 ARG A 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.89 seconds wall clock time: 40 minutes 5.11 seconds (2405.11 seconds total)